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<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt - The GenomeTools genome analysis system.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt</strong> [option &#8230;] [tool | script] [argument &#8230;]</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-i</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
enter interactive mode after executing <em>tool</em> or <em>script</em>
</p>
</dd>
<dt class="hdlist1">
<strong>-q</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
suppress warnings
</p>
</dd>
<dt class="hdlist1">
<strong>-test</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
perform unit tests and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-seed</strong> [<em>value</em>]
</dt>
<dd>
<p>
set seed for random number generator manually.
0 generates a seed from current time and process id
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
<div class="paragraph"><p>Tools:</p></div>
<div class="ulist"><ul>
<li>
<p>
<strong>bed_to_gff3</strong>
</p>
</li>
<li>
<p>
<strong>cds</strong>
</p>
</li>
<li>
<p>
<strong>chain2dim</strong>
</p>
</li>
<li>
<p>
<strong>chseqids</strong>
</p>
</li>
<li>
<p>
<strong>clean</strong>
</p>
</li>
<li>
<p>
<strong>compreads</strong>
</p>
</li>
<li>
<p>
<strong>condenseq</strong>
</p>
</li>
<li>
<p>
<strong>congruence</strong>
</p>
</li>
<li>
<p>
<strong>convertseq</strong>
</p>
</li>
<li>
<p>
<strong>csa</strong>
</p>
</li>
<li>
<p>
<strong>dot</strong>
</p>
</li>
<li>
<p>
<strong>dupfeat</strong>
</p>
</li>
<li>
<p>
<strong>encseq</strong>
</p>
</li>
<li>
<p>
<strong>encseq2spm</strong>
</p>
</li>
<li>
<p>
<strong>eval</strong>
</p>
</li>
<li>
<p>
<strong>extractfeat</strong>
</p>
</li>
<li>
<p>
<strong>extractseq</strong>
</p>
</li>
<li>
<p>
<strong>fastq_sample</strong>
</p>
</li>
<li>
<p>
<strong>featureindex</strong>
</p>
</li>
<li>
<p>
<strong>fingerprint</strong>
</p>
</li>
<li>
<p>
<strong>genomediff</strong>
</p>
</li>
<li>
<p>
<strong>gff3</strong>
</p>
</li>
<li>
<p>
<strong>gff3_to_gtf</strong>
</p>
</li>
<li>
<p>
<strong>gff3validator</strong>
</p>
</li>
<li>
<p>
<strong>gtf_to_gff3</strong>
</p>
</li>
<li>
<p>
<strong>hop</strong>
</p>
</li>
<li>
<p>
<strong>id_to_md5</strong>
</p>
</li>
<li>
<p>
<strong>inlineseq_add</strong>
</p>
</li>
<li>
<p>
<strong>inlineseq_split</strong>
</p>
</li>
<li>
<p>
<strong>interfeat</strong>
</p>
</li>
<li>
<p>
<strong>loccheck</strong>
</p>
</li>
<li>
<p>
<strong>ltrclustering</strong>
</p>
</li>
<li>
<p>
<strong>ltrdigest</strong>
</p>
</li>
<li>
<p>
<strong>ltrharvest</strong>
</p>
</li>
<li>
<p>
<strong>matchtool</strong>
</p>
</li>
<li>
<p>
<strong>matstat</strong>
</p>
</li>
<li>
<p>
<strong>md5_to_id</strong>
</p>
</li>
<li>
<p>
<strong>merge</strong>
</p>
</li>
<li>
<p>
<strong>mergefeat</strong>
</p>
</li>
<li>
<p>
<strong>mgth</strong>
</p>
</li>
<li>
<p>
<strong>mkfeatureindex</strong>
</p>
</li>
<li>
<p>
<strong>mkfmindex</strong>
</p>
</li>
<li>
<p>
<strong>mmapandread</strong>
</p>
</li>
<li>
<p>
<strong>orffinder</strong>
</p>
</li>
<li>
<p>
<strong>packedindex</strong>
</p>
</li>
<li>
<p>
<strong>prebwt</strong>
</p>
</li>
<li>
<p>
<strong>readjoiner</strong>
</p>
</li>
<li>
<p>
<strong>repfind</strong>
</p>
</li>
<li>
<p>
<strong>scriptfilter</strong>
</p>
</li>
<li>
<p>
<strong>seed_extend</strong>
</p>
</li>
<li>
<p>
<strong>select</strong>
</p>
</li>
<li>
<p>
<strong>seq</strong>
</p>
</li>
<li>
<p>
<strong>seqfilter</strong>
</p>
</li>
<li>
<p>
<strong>seqids</strong>
</p>
</li>
<li>
<p>
<strong>seqmutate</strong>
</p>
</li>
<li>
<p>
<strong>seqorder</strong>
</p>
</li>
<li>
<p>
<strong>seqstat</strong>
</p>
</li>
<li>
<p>
<strong>seqtransform</strong>
</p>
</li>
<li>
<p>
<strong>seqtranslate</strong>
</p>
</li>
<li>
<p>
<strong>sequniq</strong>
</p>
</li>
<li>
<p>
<strong>shredder</strong>
</p>
</li>
<li>
<p>
<strong>shulengthdist</strong>
</p>
</li>
<li>
<p>
<strong>simreads</strong>
</p>
</li>
<li>
<p>
<strong>sketch</strong>
</p>
</li>
<li>
<p>
<strong>sketch_page</strong>
</p>
</li>
<li>
<p>
<strong>snpper</strong>
</p>
</li>
<li>
<p>
<strong>speck</strong>
</p>
</li>
<li>
<p>
<strong>splicesiteinfo</strong>
</p>
</li>
<li>
<p>
<strong>splitfasta</strong>
</p>
</li>
<li>
<p>
<strong>stat</strong>
</p>
</li>
<li>
<p>
<strong>suffixerator</strong>
</p>
</li>
<li>
<p>
<strong>tagerator</strong>
</p>
</li>
<li>
<p>
<strong>tallymer</strong>
</p>
</li>
<li>
<p>
<strong>tirvish</strong>
</p>
</li>
<li>
<p>
<strong>uniq</strong>
</p>
</li>
<li>
<p>
<strong>uniquesub</strong>
</p>
</li>
<li>
<p>
<strong>wtree</strong>
</p>
</li>
</ul></div>
<div class="paragraph"><p>Set the environment variable <tt>GT_MEM_BOOKKEEPING=on</tt> to enable memory
bookkeeping (e.g., like this: <tt>env GT_MEM_BOOKKEEPING=on gt</tt>).</p></div>
<div class="paragraph"><p>Set the environment variable <tt>GT_ENV_OPTIONS=-spacepeak</tt> to show a spacepeak
after program run.
Set the environment variable <tt>GT_ENV_OPTIONS=-showtime</tt> to show processing times
for some program parts if implemented.</p></div>
<div class="paragraph"><p>Set the environment variable <tt>GT_SEED</tt> to an integer value to supply a seed for
the random number generator. Can be overridden by the <tt>-seed</tt> option.</p></div>
<div class="paragraph"><p>Combinations are possible. Running the <tt>gt</tt> binary with <tt>GT_ENV_OPTIONS=-help</tt>
shows all possible "environment options".</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
</div>
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